JIC Genome Lab: Transposons for Functional
Genomics
Jonathan Clarke, Sean Walsh, Mike Bevan and Jonathan Jones
The John Innes Centre Genome Lab supports the utilization of transposon insertions,
developed by GARNET, for functional genomics applications. Four populations of
Arabidopsis lines containing transposon insertions were generated by GARNET and
are freely available from NASC. The transposon lines offer resources for forward and
reverse genetic screens in the Columbia-0 and Landsberg erecta ecotypes. Special
features include: inducible over-expression, gene traps for expression analysis and
enhancer traps for mis-expression in addition to simple knock out mutants.
The transposon insertion sites have been sequenced, integrating the transposon lines
with the gene models. These may be viewed at ATIdb or NASC AtEmsembl. Gene
expression patterns identified within the GARNET Gene Trap (GGT) collection have
been integrated into ATIdb. Patterns can be searched and retrieved using a simple
Ontology at ATIdb Gene Traps.
The John Innes Centre Genome Lab will shortly be releasing lines via NASC for the
remobilization of SM lines and the inducible over-expression of SM lines. Full
support including protocols and advice will be available.
A new insertion site verification service for transposon and T-DNA lines will be
available shortly to screen putative insertions within defined genes and isolate
homozygous lines. The long term goal of this service will be to establish unigene
knockout sets for the community.
GARNET Collections
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The SM collection of single copy dSpm insertions, produced by Dr. Jonathan
Clarke (GARNET) from the SLAT collection of Prof. Jonathan Jones
(Sainsbury laboratory BBSRC grant 83/GAT9113 - GAIT; EU grant
BI04CT95183 - AIMS). (Columbia-0)
The ACTIVATE (AT) collection, produced by Dr. Jonathan Clarke and Dr.
George Coupland at the JIC (BBSRC grant PAG01523 - PAGA; EU grant
BIO4CT95183 - AIMS), which was generated by the mobilization of an
Activation Ds transposable element. (Landsberg erecta)
The GARNET Gene Traps (GGT) collection, produced by Dr. Jonathan
Clarke and Prof. Mike Bevan at the JIC (BBSRC grant FGT11378; EU grant
QLG2CT1999-00351 - EXOTIC), which was generated by the mobilization of
a Gene-Trap Ds transposable element. (Landsberg erecta)
The GARNET Mis Expression Enhancer Traps (GMT) collection produced
by Dr Jonathan Clarke at the JIC and Dr. Ian Moore at Oxford University
(BBSRC grant FGT11321), which was generated by the mobilization of Misexpression Enhancer Trap Ds transposable element. (Landsberg erecta)
For further details of the lines and applications contact Jonathan Clarke
For ATIdb enquiries contact Sean Walsh